Align GtsD (GLcK), component of Glucose porter, GtsABCD (characterized)
to candidate WP_011385763.1 AMB_RS17210 molybdenum import ATP-binding protein ModC
Query= TCDB::Q88P35 (384 letters) >NCBI__GCF_000009985.1:WP_011385763.1 Length = 363 Score = 146 bits (369), Expect = 8e-40 Identities = 103/304 (33%), Positives = 160/304 (52%), Gaps = 31/304 (10%) Query: 23 DIQLSIKDGEFLILVGPSGCGKSTLMNCIAGLEQITGGAI------LIDEQDVSGMSPKD 76 D++LS G L G SG GK++++N +AGL + G+I L D + + P+ Sbjct: 16 DVRLSAGPG-VTALYGRSGSGKTSVINMVAGLSRPDEGSISVDGRVLFDSRSGIDLPPEA 74 Query: 77 RDIAMVFQSYALYPTMSVRENIEFGLKIRKLPQAAIDEEVARVAKLLQIEHLLARKPAQL 136 R + VFQ + L+P +SVR N+EFG K+ LP A + + +V +LL IE LL R+PA+L Sbjct: 75 RRLGYVFQEHRLFPHLSVRGNLEFGQKL--LPSAERTQSLDKVVELLGIESLLDRRPAKL 132 Query: 137 SGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKLMHQRLKTTTVYVTHDQ 196 SGG++QRVA+GRAL P+I L DEPL+ LD + E+ + + +R +YV+H Sbjct: 133 SGGEKQRVAIGRALLASPRILLMDEPLAALDPARKAEVLPFIAQLARRFSVPILYVSHSM 192 Query: 197 IEAMTLGDKVAVMKDGIIQQFGTPQQIYNDP----------ANQFVASFIGSPPMNFIPV 246 E + L D +A+M G + G + + DP A + + + S F Sbjct: 193 DEVLRLADTLALMDGGKVAASGPLESLMGDPGLRPLTGRYEAGAVIGAVVSSHDSGFGIS 252 Query: 247 RLARQDGRLLALLDSGQARCELPLG-EAADALEGREIILGIR-PEQIALGAADGNGLPAI 304 RLA G L+ R ELP+G + + R++ + I P+++++ N LPAI Sbjct: 253 RLAFDGGTLIV------GRSELPVGAKVRLRIHARDVAIAIEPPDRVSI----RNVLPAI 302 Query: 305 RAEV 308 V Sbjct: 303 VVSV 306 Lambda K H 0.320 0.137 0.391 Gapped Lambda K H 0.267 0.0410 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 1 Number of Hits to DB: 351 Number of extensions: 16 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 384 Length of database: 363 Length adjustment: 30 Effective length of query: 354 Effective length of database: 333 Effective search space: 117882 Effective search space used: 117882 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory